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- PDB-5ea7: Crystal Structure of Inhibitor BMS-433771 in Complex with Prefusi... -

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Basic information

Entry
Database: PDB / ID: 5ea7
TitleCrystal Structure of Inhibitor BMS-433771 in Complex with Prefusion RSV F Glycoprotein
ComponentsFusion glycoprotein F0
KeywordsCELL INVASION/INHIBITOR / Class I viral fusion protein / fusion / respiratory syncytial virus / prefusion / viral protein / fusion inhibitor / CELL INVASION-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Chem-5NO / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 Å
AuthorsBattles, M.B. / McLellan, J.S. / Arnoult, E. / Roymans, D. / Langedijk, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Charles H. Hood Foundation United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Molecular mechanism of respiratory syncytial virus fusion inhibitors.
Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / ...Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / Arnoult, E. / Peeples, M.E. / Roymans, D. / McLellan, J.S.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2838
Polymers63,2181
Non-polymers1,0657
Water43224
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,85024
Polymers189,6553
Non-polymers3,19521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16960 Å2
ΔGint-259 kcal/mol
Surface area50910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.590, 169.590, 169.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11F-705-

HOH

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 63218.344 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain (UNP residues 1-513) / Mutation: S190F, V207L, S155C, S290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Plasmid: p(alpha)H / Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-5NO / 1-cyclopropyl-3-[[1-(4-oxidanylbutyl)benzimidazol-2-yl]methyl]imidazo[4,5-c]pyridin-2-one / BMS-433771


Mass: 377.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.54 M potassium/sodium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→41.13 Å / Num. obs: 20080 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.074 / Net I/σ(I): 9.1 / Num. measured all: 178444 / Scaling rejects: 62
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.85-39.21.66922608028500.5420.585100
9.01-41.137.70.0520.857257420.9970.01898.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MMS

4mms


Resolution: 2.851→41.13 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 979 4.89 %Random selection
Rwork0.196 19060 --
obs0.1982 20039 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.4 Å2 / Biso mean: 67.3919 Å2 / Biso min: 29.49 Å2
Refinement stepCycle: final / Resolution: 2.851→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 66 24 3466
Biso mean--121.01 51.19 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063496
X-RAY DIFFRACTIONf_angle_d0.9794731
X-RAY DIFFRACTIONf_chiral_restr0.036565
X-RAY DIFFRACTIONf_plane_restr0.004582
X-RAY DIFFRACTIONf_dihedral_angle_d15.7781275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8508-3.0010.37971530.307426492802
3.001-3.1890.28681340.255626502784
3.189-3.43510.28951360.23326782814
3.4351-3.78050.22111350.189726902825
3.7805-4.32710.21111270.180927302857
4.3271-5.44970.21021460.157327452891
5.4497-41.13590.23521480.188229183066
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1866-1.977-2.04296.84543.17462.2224-0.2248-0.1838-0.1690.61630.12990.29090.1920.23230.08330.44140.0026-0.02120.54890.06730.28852.95885.935732.4098
24.18981.14943.25370.97192.05394.44960.05260.6421-0.6691-0.26830.12810.02010.3232-0.0544-0.27910.7782-0.0038-0.04840.6202-0.17180.72865.2391-17.2988-9.9043
34.3229-0.04650.52090.94931.44564.5312-0.02220.3258-1.1339-0.36980.3169-0.04480.63210.6707-0.31470.58120.0573-0.0420.4782-0.01680.632518.9348-12.58689.0667
46.80210.6220.48145.01670.01693.03340.33840.5873-1.7039-0.1624-0.2517-0.25460.56890.0924-0.02691.1951-0.0855-0.13540.5388-0.12121.1693.7493-27.5889-3.4058
53.3742-0.59580.25990.74970.273.73390.03050.0392-0.566-0.164-0.02690.3710.4998-0.7244-0.06420.6927-0.1332-0.10980.4816-0.04680.74121.4184-14.47493.3481
66.6593-0.0347-2.06372.90940.29076.0140.29910.2209-0.320.0809-0.09470.07950.5716-0.3133-0.09520.5572-0.1166-0.19910.3482-0.00770.59396.2356-13.868310.5688
72.70890.39860.11887.91583.65553.228-0.028-0.29760.08460.0294-0.10740.4152-0.2216-0.17960.13690.3298-0.0001-0.0340.4050.02220.3358.604711.388130.5006
89.44425.02794.48196.75923.44657.5624-0.36750.04960.2126-0.18890.01710.5849-0.0712-0.08450.27760.42330.035-0.01420.4026-0.03140.50387.4451.134124.3382
94.3641-0.2931.11514.52471.71911.72210.0568-0.6895-0.01650.60140.0693-0.40650.1509-0.0795-0.11370.4650.0351-0.00750.51950.00730.34799.372417.269834.4388
108.3081-0.0343-2.28917.2591-3.21945.23380.2038-0.10510.52780.0829-0.01130.7027-0.2163-0.5426-0.23050.4890.10030.04720.448-0.09270.4458-8.515826.521729.3648
116.6572-0.67644.48143.268-0.59379.4404-0.1939-0.5869-0.16910.261-0.07690.68320.2179-0.73320.26060.40920.08460.12370.4269-0.03120.4636-7.029217.899730.2423
126.043.74830.45229.3355-0.3553.91090.4205-0.64790.82470.9191-0.6332-1.5984-0.49990.7257-0.10190.7449-0.0411-0.21850.6323-0.03940.83723.53729.1438.601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 27 through 52 )F0
2X-RAY DIFFRACTION2chain 'F' and (resid 53 through 98 )F0
3X-RAY DIFFRACTION3chain 'F' and (resid 137 through 170 )F0
4X-RAY DIFFRACTION4chain 'F' and (resid 171 through 219 )F0
5X-RAY DIFFRACTION5chain 'F' and (resid 220 through 267 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 268 through 302 )F0
7X-RAY DIFFRACTION7chain 'F' and (resid 303 through 352 )F0
8X-RAY DIFFRACTION8chain 'F' and (resid 353 through 376 )F0
9X-RAY DIFFRACTION9chain 'F' and (resid 377 through 416 )F0
10X-RAY DIFFRACTION10chain 'F' and (resid 417 through 443 )F0
11X-RAY DIFFRACTION11chain 'F' and (resid 444 through 473 )F0
12X-RAY DIFFRACTION12chain 'F' and (resid 474 through 512 )F0

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